'The Holy Father expressed his sorrow at the anguish caused by the deplorable conduct of some members of the Church,' when he met a delegation of Native Canadian representatives at the Vatican, a Holy See statement said.
The pontiff 'offered his sympathy and prayerful solidarity,' to the group headed by the Grand Chief of the Assembly of First Nations of Canada, Phil Fontaine, the Vatican said.
Native Canadians and Americans, also known as Indians, inhabited the North American continent when European settlers first began arriving in the wake of Christopher Columbus' 'discovery' of the New World in 1492.
In the late 19th century, Canadian authorities began taking Native Canadian children away from their families and placing them in so- called residential schools, many of which were run by the Catholic Church, the Anglican Church, the United Church and the Presbyterian Church.
An estimated 100,000 attended these schools by the time they were closed in the early 1980s, according to a statement by the Catholic Bishop Conference of Canada.
Many former students of these schools, alleging abuses, filed lawsuits against the Canadian government and the religious organizations. They also demanded a formal apologies for the treatment received in the schools.
Following a settlement agreement, billions of dollars were transferred to Native Canadian communities.
The Catholic Church's contributed some 79 million dollars, the Canadian Catholic bishops said in their statement.
In 2008, Canadian Prime Minister Stephen Harper issued a formal apology in the Canadian Parliament last year, calling the treatment of children at the schools a sad chapter in the country's history.
The United, Presbyterian and Anglican churches have all apologized for their roles in the abuse.
Fontaine, had asked in the past that the Catholic Church take a similar stance, citing Benedict's apologies over a clergy sex abuse scandals when he visited America and Australia in 2008.
On Wednesday Benedict said 'acts of abuse cannot be tolerated in society. He prayed that all those affected would experience healing, and he encouraged First Nations Peoples to continue to move forward with renewed hope,' the Vatican statement said.
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